nf-core/sammyseq
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 5 columns, and a header row. See usage docs.
Path to comma-separated file containing the sample names for the desired paired comparisons.
stringYou will need to create a comparisons file with information about the desired comparisons in your experiment before running the pipeline. It has to be a comma-separated file with 2 columns: one for the first sample to compare and the second one to sample against which to do it. The sample names must match the sample names present in the first column of the samplesheet (--input parameter).
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleantrueDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomesSpecify aligner to be used to map reads to reference genome.
stringSpecify the program to use for read trimming
stringPath to directory or tar.gz archive for pre-built BWA index.
stringIf generated by the pipeline save the aligner index (e.g. BWA) in the results directory.
booleanIf the index generated by the aligner is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times.
Path to directory or tar.gz archive for pre-built bowtie2 index.
stringIf generated by the pipeline save the BWA index in the results directory.
booleanA BED or GTF file containing regions that should be excluded from all analyses.
stringCurrently this works by rejecting genomic chunks that happen to overlap an entry. Consequently, for BAM files, if a read partially overlaps a blacklisted region or a fragment spans over it, then the read/fragment might still be considered. Please note that you should adjust the effective genome size, if relevant.
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Specify after which step the pipeline should stop.
stringbooleanSuffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDefines how much the reads should be extended
integerbw_resolution (expressed in base pairs) for genome coverage calculation (default 1).
integer1Method selecte to perform the normalizazion
stringEstimated genome size to performing the normalization
integerA list of space-delimited chromosome names containing those chromosomes that should be excluded for computing the normalization
stringIf set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate\u2019s position also has to coincide to ignore a read
boolean-L options filter the alignments that will be included in the output to only those alignments that match certain criteria.
stringkip alignments with MAPQ smaller than 'value' (1 default).
integer1If set filter reads based on specific flags. Flags represent various properties of a read, such as whether it's mapped, paired, or properly aligned (default 1540)
integer1540Region of the genome to limit the operation to - this is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example –region chr10 or –region chr10:456700:891000.
stringThe number of bins that are sampled from the genome, for which the overlapping number of reads is computed. (Default: 500000)
integer500000Deeptools multiBamSummary bam bin size (Default 50000).
integerDeeptools Correlation Plot statistical calculation method
stringFragment size parameter for single-end data. When set to a positive value, it enables the --extendReads option in DeepTools, extending reads to the specified length. This parameter is only used for single-end data processing and does not affect paired-end data analysis.
integer100Optionally provide chromosome sizes file as input
stringOptionally provide FASTA index (.fai) file as input
stringPath to GTF annotation file.
stringPath to BED file containing gene intervals. This will be created from the GTF file if not specified.
string